BreakPointer

What is BreakPointer?

BreakPointer is a tool to pinpoint rearrangement breakpoints using paired end reads.

How does it work?

In brief, BreakPointer consists of five steps, shown in the sketch below:

dRanger predicts approximate somatic rearrangement.

BreakPointer fishes for reads that span both sides of a putative breakpoint.

The reads are aligned by a modified Smith-Waterman algorithm.

Each breakpoint is called and assigned quality score, and the segments are fused acorrdingly to deduce the cancer genome.

All the candidate split reads in the list are being aligned to the newly fused sequence. Breakpoints, fused sequences and the reads that support them are reported, and exported to IGV for easy view (actual IGV example is shown at the bottom)

How to Cite BreakPointer?

BreakPointer users may publish or otherwise publicly disclose the results of using BreakPointer. Please acknowledge BreakPointer in your publications by citing the following reference: